Alright so I recently installed Serenity which has a built-in mapper in it. After much trouble shooting (deleting the mapper directory files, restarting again and again. Okay so not much troubleshooting but crossing fingers and hoping) I can't seem to get it fixed.
So as you can see:
The consoled mapper shows exits N, NE, SW, W
The IG mapper shows exits N,NE, SW,IN (which matches up to the display using the map command)
And pretty much the rooms are all higgle-piggle and there are random terrain patches within the city. When I walk around the map follows smoothly, not jumping around which would usually signify it being confused.